EMD-5896

Single-particle
4.9 Å
EMD-5896
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Deposition: 09/02/2014
Map released: 04/06/2014
Last modified: 04/06/2014
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EMD-5896
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 3j6f summary report (pdf.gz) Map and 3j6f FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo EM density of GDP-bound dynamic microtubules

EMD-5896

Single-particle
4.9 Å
EMD-5896
3D View Gallery
Deposition: 09/02/2014
Map released: 04/06/2014
Last modified: 04/06/2014
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Helical Array
Specimen preparation [1]
Concentration: 0.25 mg/mL
Buffer
pH: 6.8
Details: 80mM PIPES, 1mM EGTA, 1mM MgCl2, 1mM DTT, 0.05% Nonidet P-40
Grid
Details: 400 mesh C-flat 1.2/1.3, glow discharged in Edwards carbon evaporator
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 90.4 K
Instrument: FEI VITROBOT MARK II
Method: The grid was blotted for 2 seconds before plunging.
Microscopy [1]
Microscope: FEI TITAN
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 1.4 µm - 3.5 µm
Nominal magnification: 72000.0
Calibrated magnification: 72000.0
Specimen holder model: GATAN LIQUID NITROGEN
Specimen holder details: Gatan 626 holder
Alignment procedure: LEGACY (Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnifacation., Electron beam tilt params: )
Minimum tilt angle: 0
Maximum tilt angle: 0
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: OTHER
Sampling interval: 6.35 µm
Number of real images: 219
Average electron dose per image: 25.0 e/Å2
Bits per pixel: 16.0
Image processing [1]
Details: Initial alignments performed with EMAN2/SPARX, including refinement of helical parameters with the IHRSR programs of Egelman. Final alignment and reconstruction performed with FREALIGN.
Final reconstruction
Resolution: 4.9 Å ( BY AUTHOR)
Resolution method: OTHER
Number of images used: 54445
Algorithm: OTHER
Details:
⌯ Applied Symmetry
ΔΖ: 8.82 Å
ΔΦ: 25.76°
Axial symmetry: C1
Software [1]
Name Version Details
FREALIGN - -
CTF correction
Details:Ctftilt
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Cryo-EM reconstruction of dynamic GDP-bound microtubule
Details: ::::EMDATABANK.org::::EMD-5896::::
⬡ Geometry
X Y Z
Dimensions 110 66 162
Origin -55 -33 -81
Spacing 66 110 162
Voxel size 1.7399999 Å 1.74 Å 1.74 Å
Contour list
Primary Level Source
True 4.0 EMDB